RetrogeneDB ID:

retro_hsap_3983

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:87516052..87516865(+)
Located in intron of:ENSG00000176623
Retrocopy
information
Ensembl ID:ENSG00000254088
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC2A3
Ensembl ID:ENSG00000059804
Aliases:SLC2A3, GLUT3
Description:solute carrier family 2 (facilitated glucose transporter), member 3 [Source:HGNC Symbol;Acc:11007]


Retrocopy-Parental alignment summary:






>retro_hsap_3983
CTTTATCAACCACTTTTTGACAGGTGCAATTCAATGCTTATCGTCAACCTGTTGGCTGTCTCTGGTGGCTGCCTTATGGG
ATTGTGTAAAGCAGCTGAGTTGGTTGAAATGCTGACCCTGGGCTGCTTGGTTATTGGCCTCTTCTGTGGACTGTGCACAG
GTTTTATGCCCATGTACATTGGAGAGATCTCAGCTACTGCCCTGCAGGGTACCTTTGGCACTCTCAACCAGCTGGGCATC
ATTGTCAGAATTCTGGTGGCCCAGATCTTTGGTCTGGAATTCAAATTCATCCTTGGGTCTGAAGAGCTATGGCCGGTATT
ATTGGGCTTTACCATCCTTCCTGCTATCCTACAAAGTGCAGCCCTTCCATTTTGCCCTGAAAGTCCCAGGTTTTTGCTCA
TTAACAGAAAAGAAGAGGAGAATGCTAAGTAGATCCTCCAGCAGTTGTGGGGCACCCAGGATGTATCCCAAGACAACCAG
GAGATGCAAGATGAGAGTGCAAGGATGTCACAAGAAAAGCAAGTCACCGTGCTGGAGTTCTTTAGAGTATCCAGCTACCA
ACAGCCAATCATCATTTCCATTGTGCTCCAGCTCTCTCGACAGCTCTCTGGAATCAATGTTGTGTTCTATTACTCAACAG
GAATCTTCAAGGATGCAGGTGTTCAAGAGCCCATCTATGCCACCATTGGTGCACGTGTGTTTAATACTATCTTCACTGTA
GTTTCCCTATTTCTGCTGCAAAGGGCAGGAAGGCGGACCCTGCATATGATAGGCCTTGGAGGGATGGCTTTTTGTTCCAT
GCTCATGACTGTT

ORF - retro_hsap_3983 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.08 %
Parental protein coverage: 54.23 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLVIGLFCGLCTGFVPMYIGEISPTALRG
L....F.R.NSMLIVNLLAV.GGC.MGLCK.A..VEML.LG.LVIGLFCGLCTGF.PMYIGEIS.TAL.G
RetrocopyLYQPLFDRCNSMLIVNLLAVSGGCLMGLCKAAELVEMLTLGCLVIGLFCGLCTGFMPMYIGEISATALQG
ParentalAFGTLNQLGIVVGILVAQIFGLEF--ILGSEELWPLLLGFTILPAILQSAALPFCPESPRFLLINRKEEE
.FGTLNQLGI.V.ILVAQIFGLEF..ILGSEELWP.LLGFTILPAILQSAALPFCPESPRFLLINRKEEE
RetrocopyTFGTLNQLGIIVRILVAQIFGLEFKFILGSEELWPVLLGFTILPAILQSAALPFCPESPRFLLINRKEEE
ParentalNAKQILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQLSGINAVFY
NAK.ILQ.LWGTQDVSQD.QEM.DESARMSQEKQVTVLE.FRVSSY.QPIIISIVLQLS.QLSGIN.VFY
RetrocopyNAK*ILQQLWGTQDVSQDNQEMQDESARMSQEKQVTVLEFFRVSSYQQPIIISIVLQLSRQLSGINVVFY
ParentalYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTV
YSTGIFKDAGVQEPIYATIGA.V.NTIFTVVSLFL..RAGRRTLHMIGLGGMAFCS.LMTV
RetrocopyYSTGIFKDAGVQEPIYATIGARVFNTIFTVVSLFLLQRAGRRTLHMIGLGGMAFCSMLMTV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .02 RPM 455 .03 RPM
bodymap2_adrenal 0 .25 RPM 77 .33 RPM
bodymap2_brain 0 .05 RPM 80 .75 RPM
bodymap2_breast 0 .27 RPM 68 .41 RPM
bodymap2_colon 0 .00 RPM 204 .34 RPM
bodymap2_heart 0 .04 RPM 19 .66 RPM
bodymap2_kidney 0 .31 RPM 8 .58 RPM
bodymap2_liver 0 .04 RPM 5 .68 RPM
bodymap2_lung 0 .00 RPM 433 .12 RPM
bodymap2_lymph_node 0 .02 RPM 189 .26 RPM
bodymap2_ovary 0 .15 RPM 72 .17 RPM
bodymap2_prostate 0 .00 RPM 228 .14 RPM
bodymap2_skeletal_muscle 0 .00 RPM 48 .56 RPM
bodymap2_testis 0 .00 RPM 64 .06 RPM
bodymap2_thyroid 0 .04 RPM 25 .74 RPM
bodymap2_white_blood_cells 0 .00 RPM 187 .05 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3983 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3983 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_186926414 libraries325 libraries519 libraries199 libraries372 libraries

The graphical summary, for retro_hsap_3983 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_3983 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3983 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2703
Pongo abelii retro_pabe_3274
Macaca mulatta retro_mmul_2301
Parental genes homology:
Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000045562 retrocopies
retro_btau_708, retro_btau_709,
Callithrix jacchus ENSCJAG000000189881 retrocopy
retro_cjac_446,
Cavia porcellus ENSCPOG000000030741 retrocopy
retro_cpor_761,
Cavia porcellus ENSCPOG000000098341 retrocopy
retro_cpor_760,
Cavia porcellus ENSCPOG000000112951 retrocopy
retro_cpor_587,
Felis catus ENSFCAG000000016251 retrocopy
retro_fcat_1924,
Homo sapiens ENSG00000059804 2 retrocopies
retro_hsap_3983 , retro_hsap_401,
Gorilla gorilla ENSGGOG000000168131 retrocopy
retro_ggor_398,
Macaca mulatta ENSMMUG000000004392 retrocopies
retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys ENSNLEG000000269032 retrocopies
retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus ENSOCUG000000085751 retrocopy
retro_ocun_352,
Pongo abelii ENSPPYG000000042351 retrocopy
retro_pabe_315,
Pan troglodytes ENSPTRG000000046261 retrocopy
retro_ptro_307,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.13 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .12 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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